12202021 Taiwan International Graduate Program Academia Sinica 2

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12/20/2021 Taiwan International Graduate Program Academia Sinica 2

12/20/2021 Taiwan International Graduate Program Academia Sinica 2

Fig 1. Metabolic Pathways Ex. PASy, http: //www. expasy. org /cgi-bin/show_thumbnails. pl, founded by

Fig 1. Metabolic Pathways Ex. PASy, http: //www. expasy. org /cgi-bin/show_thumbnails. pl, founded by Roche Applied Science. 12/20/2021 Taiwan International Graduate Program Academia Sinica 3

Metabolic Pathways It is the pathway to show to generate energy and remove metabolite

Metabolic Pathways It is the pathway to show to generate energy and remove metabolite for a body. Signal Transduction Pathways It is the pathway to show to control the behaviors of a cell in terms of time and location with the signals like hormones. Regulatory Pathways (Gene Regulatory Network) It is the pathway to show to adapt to the change of environment based on the principles encoded in hereditary materials (e. g. DNA). 12/20/2021 Taiwan International Graduate Program Academia Sinica 4

Signal Transduction 1 Glucoses + 2 ATP Metabolism Regulation 12/20/2021 Taiwan International Graduate Program

Signal Transduction 1 Glucoses + 2 ATP Metabolism Regulation 12/20/2021 Taiwan International Graduate Program Academia Sinica 4 ATP + 2 Pyruvate + 2 NADH 5

To understand the mechanism of organism • It provides the guidance for biologists to

To understand the mechanism of organism • It provides the guidance for biologists to design experiments. • It helps pharmacist to design drugs easier. • It makes us know the difference of mechanism between species. Enable us to do the simulation • It saves time and money for biologists to do experiments. • It predicts the behaviors by a special treatment for an organism. • It waives the dangers to try a new drug on patients. 12/20/2021 Taiwan International Graduate Program Academia Sinica 6

Overviews of Pathway Studies Literature Mining Pathway Diagrams Graphical Modelers Pathway Databases Pathway Representation

Overviews of Pathway Studies Literature Mining Pathway Diagrams Graphical Modelers Pathway Databases Pathway Representation Management Tools for Pathway Database Integration Standard for Exchanging Pathways Pathway Querying & Reasoning Simulation 12/20/2021 Taiwan International Graduate Program Academia Sinica 7

Data Accumulation Data Repository Data Exchange Data Inference Literature Mining Pathway Databases Database Integration

Data Accumulation Data Repository Data Exchange Data Inference Literature Mining Pathway Databases Database Integration Pathway Query Pathway Diagrams Pathway Representation Standard Format for Pathways Pathway Reasoning Graphical Modelers Simulation Cell Behaviors Simulation Management Tools Hot Issues 12/20/2021 Taiwan International Graduate Program Academia Sinica 8

ACTIVATOR activate ACTIVATEE l RAF 6 NF-kappa. B l Lck autophosphorylation at Tyr 394

ACTIVATOR activate ACTIVATEE l RAF 6 NF-kappa. B l Lck autophosphorylation at Tyr 394 l Anandamide vanilloid receptors Rap 1 GTPase stress 12/20/2021 C 3 G rho. GAP group of MAP kinases Taiwan International Graduate Program Academia Sinica 9

Moustafa M. Ghanem et al. (UK) Regular Expression Pattern Matching SVM Classifier Yizhar Regev

Moustafa M. Ghanem et al. (UK) Regular Expression Pattern Matching SVM Classifier Yizhar Regev et al. (Israel & USA) Rule-based Pattern Matching Text Mining Min Shi et al. (Singapore) Manually chosen keywords Keywords Distance B. Chen (Personal Communication) Alexander S. Yeh et al. (2003) “Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup” Bioinformatics, Vol. 19 Suppl. 1 2003, pages i 331–i 339 12/20/2021 Taiwan International Graduate Program Academia Sinica Regular Expression SVM Classifier 10

Complete Medium Minimal Medium

Complete Medium Minimal Medium

Minimal Medium plus aminoacids Minimal Medium plus vitamis Minimal Medium plus nucleotides

Minimal Medium plus aminoacids Minimal Medium plus vitamis Minimal Medium plus nucleotides

1 2 3 4 5 6 7 1 + + 2 3 4 5

1 2 3 4 5 6 7 1 + + 2 3 4 5 6 7 + + + + -

1 2 3 4 5 6 7 1 + + 2 3 4 5

1 2 3 4 5 6 7 1 + + 2 3 4 5 6 7 + + + + -

Remember the basic rule: 1 2 3 4 5 6 W - + +

Remember the basic rule: 1 2 3 4 5 6 W - + + - X - - - Y - + - - Z - - - + - - His + + +

1 2 3 4 5 6 W - + + - X - -

1 2 3 4 5 6 W - + + - X - - - Y - + - - Z - - - + - - His + + + Mutants 1 and 6 do this: they block the final step.

1 2 3 4 5 6 W - + + - X - -

1 2 3 4 5 6 W - + + - X - - - Y - + - - Z - - - + - - His + + + Thus, the pathway so far is W -> His, with 1 and 6 affecting this step.